Project Coordination
The genetics pedigree work will be carried out by Michael Blouin at Oregon State University.  This project is coordinated with the Hood River steelhead hatchery and research project, funded by Bonneville Power Administration and administered and implemented by the Oregon Department of Fish and Wildlife (Rod French and Erik Olsen, supervisor and database manager).

Location of project
Steelhead samples collected at Powerdale Dam, Hood River, under supervision of Rod French, ODFW.  All laboratory work and data analysis to be conducted in the laboratory of Michael Blouin at Oregon State University.

Background
The Hood River supports two populations of steelhead, a summer run and a winter run.  They spawn only above the Powerdale Dam, which is a complete barrier to all salmonids.  Since 1991 every adult passed above the dam has been measured, cataloged and sampled for scales.  Therefore, we have a DNA sample from every adult steelhead that went over the dam to potentially spawn in the Hood River from 1991 to the present.  Similar numbers of hatchery and wild fish have been passed above the dam during the last decade.  During the 1990's "old" domesticated hatchery stocks of each run (multiple generations in the hatchery, out-of-basin origin; hereafter Hold) were phased out, and conservation hatchery programs were started for the purpose of supplementing the two wild populations (hereafter "new" hatchery stocks, Hnew).  These samples give us the unprecedented ability to estimate, via microsatellite-based pedigree analysis, the relative total reproductive success (adult to adult production) of hatchery and wild (W) fish for two populations, over multiple brood years, and for multiple generations through F2's.  Furthermore, we can compare the relative success of two "old" hatchery stocks vs. wild fish, and two "new" hatchery stocks vs. wild.  Our preliminary analyses of samples from the 1990's show that individual parents of "old" hatchery stocks have much lower total fitness than wild fish, but that "new" stocks have fitness that is about equal to that of wild fish.  All three types of crosses produce enough returning adults that we can use their offspring (F2's) to estimate the fitness of F1's as a function of the fraction of their genome that has been through a hatchery.

Overall project goals
Estimate the reproductive success (total fitness defined as adult-to-adult production) of hatchery-origin steelhead relative to that of wild-origin steelhead that have been spawning in the Hood River.  Estimate this difference using "old" hatchery stock vs. wild, and "new" hatchery stock vs. wild.  Do the comparison for multiple brood years in order to estimate the year-to-year variance in the parameters.  To date we have compared the fitness of wild and hatchery winter run from the 1991, 1995 and 1996 run years, and for summer run from the 1995 and 1996 run years.  We propose continuing sampling and genotyping through the rest of this decade in order to generate an almost 20 year pedigree for the two runs.  From this pedigree we will obtain estimates of the mean and year-to-year variance in the relative reproductive success of hatchery vs. wild fish, parameter estimates that are critical for predicting the effects of hatchery supplementation on wild steelhead populations.  We will also use the pedigree to ask a number of other applied and basic questions.  These data will be very relevant to the question of whether successful reproduction by hatchery fish in the wild might be having negative genetic effects on the wild population.


Specific objectives for fiscal year 2006 (Oct 05 through Sept 06)

(1) Manage and supervise one year of work
(2) Genotype 3600 fish.
(3) Analyze the data in terms of relative fitness of hatchery and wild fish
(4) Produce quarterly and annual reports describing progress and results
(5) Communicate results via scientific meetings and publication


Budget Explanation for FY06

Personnel
Technician - Full time. Main person conducting the lab work, scoring the genotyper output, and maintaining the database.  Also in charge of general lab maintenance, ordering supplies, etc…

Grad student - One academic quarter.  Assists technician with lab work and database management.  

Postdoc -Full time.  Coordinates and participates in the lab work.  Analyzes data, writes manuscripts.

Principal investigator -2.5 mo. summer salary (PI is on a 9 month appointment).  Lab manager, supervises personnel, participates in data analysis and writing of reports and manuscripts.

Supplies
Genotyping at $13.0/fish.  Empirical estimate based on our usage during the first part of this project.

Misc. supplies - incidental fees such as waste disposal fees, software upgrades, replacing bad reagents, and so on, that are not accounted for in the per-fish cost of genotyping.  I can usually count on a few thousand a year in that sort of expense.

Equipment repair - equipment that breaks down is an expense that is difficult to predict, but happens regularly.  For example, last year our thermocycler broke down and needed to be replaced.  Other examples from the last few years include new cartridges and new ohm-meter for the ultra-pure water system (plus plumber salaries) that cost about $900.  A brownout ruined several pieces of equipment three years ago, freezers and refrigerators fail regularly, and our microcentrifuge had to be replaced two years ago.  If the Hydra liquid handling system needed repairs, the company would have to send someone down from Seattle to fix it.  I don't keep insurance or service contracts on my equipment because that is just too expensive.  But then I have to absorb the repairs when things break.  So although it sounds a little vague to just say $2K in unpredictable repairs, on average it is a reasonable guess.

Equipment
None

Domestic travel
Automobile trips such as to confer with ODFW co-operators or to collect samples (e.g. to Salem, Hood River, Dalles), or to meet with local colleagues such as NOAA-FISHERIES researchers in Seattle, or BPA contacts in Portland.  We use the OSU motor pool vehicles.  Amount is based on previous usage.

Scientific meetings:  It is essential that the postdoc or I meet with colleagues who are doing similar work at least once per year.  There are projects similar to ours taking place in several other locales.  It is very useful for the researchers to share information about what they are finding.